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  1. Article ; Online: Introduction to the Special Issue: The Immunopeptidome.

    Caron, Étienne / Perreault, Claude

    Seminars in immunology

    2023  Volume 69, Page(s) 101798

    MeSH term(s) Humans ; Peptides ; Proteomics
    Chemical Substances Peptides
    Language English
    Publishing date 2023-06-20
    Publishing country England
    Document type Editorial
    ZDB-ID 1018141-6
    ISSN 1096-3618 ; 1044-5323
    ISSN (online) 1096-3618
    ISSN 1044-5323
    DOI 10.1016/j.smim.2023.101798
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  2. Article ; Online: Re: Kara N. Maxwell, Heather H. Cheng, Jacquelyn Powers, et al. Inherited TP53 Variants and Risk of Prostate Cancer. Eur Urol 2022;81:243-50: Off-core Li-Fraumeni Syndrome Spectrum Cancers: Increasing Interest for Prostate Cancer?

    Sassi, Hela / Caron, Olivier / Rouleau, Etienne

    European urology

    2022  Volume 82, Issue 6, Page(s) e172–e173

    MeSH term(s) Humans ; Male ; Li-Fraumeni Syndrome/genetics ; Prostatic Neoplasms/genetics ; Germ-Line Mutation ; Tumor Suppressor Protein p53/genetics ; Genetic Predisposition to Disease
    Chemical Substances Tumor Suppressor Protein p53 ; TP53 protein, human
    Language English
    Publishing date 2022-09-22
    Publishing country Switzerland
    Document type Letter ; Comment
    ZDB-ID 193790-x
    ISSN 1873-7560 ; 1421-993X ; 0302-2838
    ISSN (online) 1873-7560 ; 1421-993X
    ISSN 0302-2838
    DOI 10.1016/j.eururo.2022.07.038
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    Zs.MO 294: Show issues

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  3. Article: Commentary: Tolerance and Resistance of

    Soares, Anaïs / Caron, François / Etienne, Manuel

    Frontiers in microbiology

    2019  Volume 10, Page(s) 2164

    Language English
    Publishing date 2019-09-18
    Publishing country Switzerland
    Document type Journal Article ; Comment
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2019.02164
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  4. Article ; Online: Scaling up robust immunopeptidomics technologies for a global T cell surveillance digital network.

    Kapoor, Saketh / Maréchal, Loïze / Sirois, Isabelle / Caron, Étienne

    The Journal of experimental medicine

    2023  Volume 221, Issue 1

    Abstract: The human immunopeptidome plays a central role in disease susceptibility and resistance. In our opinion, the development of immunopeptidomics and other peptide sequencing technologies should be prioritized during the next decade, particularly within the ... ...

    Abstract The human immunopeptidome plays a central role in disease susceptibility and resistance. In our opinion, the development of immunopeptidomics and other peptide sequencing technologies should be prioritized during the next decade, particularly within the framework of the Human Immunopeptidome Project initiative. In this context, we present bold ideas, fresh arguments, and call upon industrial partners and funding organizations to support and champion this important initiative that we believe has the potential to save countless lives in the future.
    MeSH term(s) Humans ; T-Lymphocytes ; Amino Acid Sequence
    Language English
    Publishing date 2023-11-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 218343-2
    ISSN 1540-9538 ; 0022-1007
    ISSN (online) 1540-9538
    ISSN 0022-1007
    DOI 10.1084/jem.20231739
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  5. Article ; Online: The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics.

    Huang, Xiaoxiang / Gan, Ziao / Cui, Haowei / Lan, Tian / Liu, Yansheng / Caron, Etienne / Shao, Wenguang

    Nucleic acids research

    2023  Volume 52, Issue D1, Page(s) D1062–D1071

    Abstract: The SysteMHC Atlas v1.0 was the first public repository dedicated to mass spectrometry-based immunopeptidomics. Here we introduce a newly released version of the SysteMHC Atlas v2.0 (https://systemhc.sjtu.edu.cn), a comprehensive collection of 7190 MS ... ...

    Abstract The SysteMHC Atlas v1.0 was the first public repository dedicated to mass spectrometry-based immunopeptidomics. Here we introduce a newly released version of the SysteMHC Atlas v2.0 (https://systemhc.sjtu.edu.cn), a comprehensive collection of 7190 MS files from 303 allotypes. We extended and optimized a computational pipeline that allows the identification of MHC-bound peptides carrying on unexpected post-translational modifications (PTMs), thereby resulting in 471K modified peptides identified over 60 distinct PTM types. In total, we identified approximately 1.0 million and 1.1 million unique peptides for MHC class I and class II immunopeptidomes, respectively, indicating a 6.8-fold increase and a 28-fold increase to those in v1.0. The SysteMHC Atlas v2.0 introduces several new features, including the inclusion of non-UniProt peptides, and the incorporation of several novel computational tools for FDR estimation, binding affinity prediction and motif deconvolution. Additionally, we enhanced the user interface, upgraded website framework, and provided external links to other resources related. Finally, we built and provided various spectral libraries as community resources for data mining and future immunopeptidomic and proteomic analysis. We believe that the SysteMHC Atlas v2.0 is a unique resource to provide key insights to the immunology and proteomics community and will accelerate the development of vaccines and immunotherapies.
    MeSH term(s) Mass Spectrometry ; Peptides/chemistry ; Peptides/immunology ; Protein Processing, Post-Translational ; Proteomics/methods ; Databases, Protein/standards ; Internet ; Humans ; Animals
    Chemical Substances Peptides
    Language English
    Publishing date 2023-11-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad1068
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  6. Article ; Online: Generation of HLA Allele-Specific Spectral Libraries to Identify and Quantify Immunopeptidomes by SWATH/DIA-MS.

    Kovalchik, Kevin / Hamelin, David / Caron, Etienne

    Methods in molecular biology (Clifton, N.J.)

    2021  Volume 2420, Page(s) 137–147

    Abstract: Developing a deep and comprehensive understanding of the collection of peptides presented by class I human leukocyte antigens (HLA ), collectively referred to as the immunopeptidome , is conducive to the success of a wide range of immunotherapies. The ... ...

    Abstract Developing a deep and comprehensive understanding of the collection of peptides presented by class I human leukocyte antigens (HLA ), collectively referred to as the immunopeptidome , is conducive to the success of a wide range of immunotherapies. The development of tools that enable the deconvolution of immunopeptidomes in the context of disease can help improve the specificity and effectiveness of therapeutic strategies targeting these peptides, such as adoptive T-cell therapy and vaccines. Here, we describe a computational workflow that facilitates the processing and interpretation of data-independent acquisition mass spectrometry (DIA-MS). We consider a specific variation of DIA-MS known as SWATH-MS. SWATH-MS is a promising technique that can be utilized to reproducibly characterize and quantify immunopeptidomes isolated from a wide range of biological sources. In this workflow, we use an assortment of database search engines and computational tools to build high-quality HLA allele-specific peptide spectral peptide libraries for the analysis of immunopeptidomic datasets acquired by SWATH-MS. Generating and sharing these spectral libraries are essential for the SWATH-MS technology to meet its full potential and to enable the rapid and reproducible quantification of HLA-specific peptides across multiple samples.
    MeSH term(s) Alleles ; HLA Antigens ; Humans ; Mass Spectrometry ; Peptide Library ; Peptides ; Proteome ; Proteomics
    Chemical Substances HLA Antigens ; Peptide Library ; Peptides ; Proteome
    Language English
    Publishing date 2021-12-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1936-0_11
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  7. Article ; Online: The effects of the β

    Dumont, Lauralyne / Caron, Alexandre / Richard, Gabriel / Croteau, Etienne / Fortin, Mélanie / Frisch, Frédérique / Phoenix, Serge / Dubreuil, Stéphanie / Guérin, Brigitte / Turcotte, Éric E / Carpentier, André C / Blondin, Denis P

    Acta physiologica (Oxford, England)

    2024  Volume 240, Issue 5, Page(s) e14127

    Abstract: Aim: Pharmacological stimulation of human brown adipose tissue (BAT) has been hindered by ineffective activation or undesirable off-target effects. Oral administration of the maximal allowable dose of mirabegron (200 mg), a β: Methods: We performed a ...

    Abstract Aim: Pharmacological stimulation of human brown adipose tissue (BAT) has been hindered by ineffective activation or undesirable off-target effects. Oral administration of the maximal allowable dose of mirabegron (200 mg), a β
    Methods: We performed a randomized crossover trial (NCT04823442) in 8 lean men. Mirabegron (200 mg) was administered orally with or without the β
    Results: Compared to room temperature, mirabegron alone increased BAT oxidative metabolism (0.84 ± 0.46 vs. 1.79 ± 0.91 min
    Conclusion: The administration of bisoprolol decreases the adverse cardiovascular effects of mirabegron. However, the provided dose also blunted the mirabegron-stimulated increase in BAT lipolysis, thermogenesis, and glucose uptake. The attenuation in BAT blood flow induced by the large dose of bisoprolol may have limited BAT thermogenesis.
    Language English
    Publishing date 2024-03-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2218636-0
    ISSN 1748-1716 ; 1748-1708
    ISSN (online) 1748-1716
    ISSN 1748-1708
    DOI 10.1111/apha.14127
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  8. Article ; Online: Phenotypic and genotypic within-host diversity of Pseudomonas aeruginosa urinary isolates.

    Cottalorda, Agnès / Dahyot, Sandrine / Soares, Anaïs / Alexandre, Kevin / Zorgniotti, Isabelle / Etienne, Manuel / Jumas-Bilak, Estelle / Pestel-Caron, Martine

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 5421

    Abstract: This study aimed to assess phenotypic and molecular inter-patient and within-host diversity of Pseudomonas aeruginosa isolates responsible for urinary tract infection (UTI) or asymptomatic bacteriuria (AB). Clinical data of 120 consecutive P. aeruginosa ... ...

    Abstract This study aimed to assess phenotypic and molecular inter-patient and within-host diversity of Pseudomonas aeruginosa isolates responsible for urinary tract infection (UTI) or asymptomatic bacteriuria (AB). Clinical data of 120 consecutive P. aeruginosa UTI (n = 40) and AB (n = 80) were prospectively analyzed. Up to five P. aeruginosa isolates per sample were collected. Antimicrobial susceptibility testing (AST) was determined for all isolates (n = 591); a subset of 358 was characterized by multilocus sequence typing. 444 isolates (75%) were non-multidrug resistant (MDR), 113 (19%) were MDR, and 34 (6%) were extensively drug resistant. A genetically highly diverse population was observed (64 sequence types [STs]), without strict correlation between genotypes and clinical settings. 35 patients (28%; 12 UTIs and 23 ABs) presented distinct antimicrobial resistance (AMR) profiles within a given urine sample, significantly associated with previous carbapenem and fluroquinolones exposure; five of them also exhibited polyclonal UTI or AB (with isolates belonging to two STs). P. aeruginosa urinary isolates of these 120 patients were highly diverse, in terms of AMR as well as genetic background. Both within-host AMR and molecular diversity can complicate AST, treatment and control of P. aeruginosa UTI.
    MeSH term(s) Drug Resistance, Multiple, Bacterial/genetics ; Genotype ; Humans ; Microbial Sensitivity Tests ; Pseudomonas Infections/drug therapy ; Pseudomonas Infections/epidemiology ; Pseudomonas aeruginosa/genetics
    Language English
    Publishing date 2022-03-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-09234-5
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  9. Article ; Online: The SysteMHC Atlas: a Computational Pipeline, a Website, and a Data Repository for Immunopeptidomic Analyses.

    Shao, Wenguang / Caron, Etienne / Pedrioli, Patrick / Aebersold, Ruedi

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2120, Page(s) 173–181

    Abstract: Mass spectrometry has emerged as the method of choice for the exploration of the immunopeptidome. Insights from the immunopeptidome promise novel cancer therapeutic approaches and a better understanding of the basic mechanisms of our immune system. To ... ...

    Abstract Mass spectrometry has emerged as the method of choice for the exploration of the immunopeptidome. Insights from the immunopeptidome promise novel cancer therapeutic approaches and a better understanding of the basic mechanisms of our immune system. To meet the computational demands from the steady gain in popularity and reach of mass spectrometry-based immunopeptidomics analysis, we created the SysteMHC Atlas project, a first-of-its-kind computational pipeline and resource repository dedicated to standardizing data analysis and public dissemination of immunopeptidomic datasets.
    MeSH term(s) Alleles ; HLA Antigens/chemistry ; HLA Antigens/genetics ; HLA Antigens/immunology ; Humans ; Internet ; Major Histocompatibility Complex ; Mass Spectrometry/methods ; Neoplasms/genetics ; Neoplasms/immunology ; Proteomics/methods ; Software
    Chemical Substances HLA Antigens
    Language English
    Publishing date 2020-03-02
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0327-7_12
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Malignant Adenomyoepithelioma of the Breast: An Unexpected Malignancy in a Lynch Syndrome Patient.

    Joyon, Natacha / Guillaume, Zoe / Ouafi, Lamia / Cotteret, Sophie / Rouleau, Etienne / Caron, Olivier / Goldbarg, Veronica / Lacroix-Triki, Magali

    International journal of surgical pathology

    2022  Volume 31, Issue 5, Page(s) 572–575

    MeSH term(s) Humans ; Female ; Adenomyoepithelioma/diagnosis ; Adenomyoepithelioma/surgery ; Adenomyoepithelioma/pathology ; Colorectal Neoplasms, Hereditary Nonpolyposis/complications ; Colorectal Neoplasms, Hereditary Nonpolyposis/diagnosis ; Breast/surgery ; Breast/pathology ; Breast Neoplasms
    Language English
    Publishing date 2022-06-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1336393-1
    ISSN 1940-2465 ; 1066-8969
    ISSN (online) 1940-2465
    ISSN 1066-8969
    DOI 10.1177/10668969221105623
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